Please post an issue: github.com/cdk/cdk
On 5 August 2017 at 01:50, Andrei Kazakov <and4li...@gmail.com> wrote:
> Hello,
>
> The "bugs" list seems to be deserted so I am posting it here. It appears
> to be an overflow issue in MDEDescriptor.java that produces zero values for
> long chains (the code is unchanged across 1.4, 1.5, and 2.0 series).
> Specifically, MDEC-22 becomes zero starting from C23 (tricosane). It is
> caused by geometric mean evaluation via direct product; replacing product
> with the sum of logs fixes the issue:
>
> private double evalCValue(int[][] distmat, int[][] codemat, int type1,
> int type2) {
> /* double lambda = 1; */
> double lambda = 0;
> double n = 0;
>
> List<Integer> v1 = new ArrayList<Integer>();
> List<Integer> v2 = new ArrayList<Integer>();
> for (int i = 0; i < codemat.length; i++) {
> if (codemat[i][0] == type1) v1.add(codemat[i][1]);
> if (codemat[i][0] == type2) v2.add(codemat[i][1]);
> }
>
> for (int i = 0; i < v1.size(); i++) {
> for (int j = 0; j < v2.size(); j++) {
> int a = v1.get(i);
> int b = v2.get(j);
> if (a == b) continue;
> double distance = distmat[a][b];
> /* lambda = lambda * distance; */
> lambda += Math.log(distance);
> n++;
> }
> }
>
> if (type1 == type2) {
> /* lambda = Math.sqrt(lambda); */
> lambda /= 2;
> n = n / 2;
> }
> if (n == 0) return 0.0;
> else
> /* return n / Math.pow(Math.pow(lambda, 1.0 / (2.0 * n)), 2);
> */
> return n / Math.exp(lambda / n);
> }
>
>
> --Andrei
>
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